Integrative transcriptomic analysis uncovers the microRNA-centric regulation of Japanese encephalitis virus infection in porcine trophoblast cells

Japanese encephalitis virus (JEV) is a mosquito-borne zoonotic virus with pig as its major amplifying host. Despite that JEV can persistently infect the placentae of pregnant sows and cause severe reproductive failures, the molecular responses and potential regulators of JEV infection in pig placenta remain unclear. Using porcine trophectoderm (pTr) cells as model, we investigated the transcriptomic changes during JEV infection, with a special focus on microRNA-centric regulation over immune genes and JEV infection. To avoid currently poor microRNA annotation for pig, we first performed small RNA-seq to achieve refined microRNA annotation, with hundreds of novel microRNAs annotated. After confirming that JEV can efficiently infect pTr cells and induce severe cytopathic effects, we conducted routine and small RNA-seq to determine the changes of mRNA and microRNA genes during JEV infection. We identified >1000 differentially expressed genes and found JEV-induced genes are tightly associated with antiviral immune responses. Moreover, we identified 94 JEV-affected microRNAs, including many with their roles on viral infection still unclear. Focusing on JEV-affected microRNAs, we constructed a microRNA-mRNA negative regulatory network, with multiple hub microRNAs and their targets inspected. Among these microRNAs, we experimentally validated that ssc-miR-149 and ssc-miR-483 both can inhibit JEV replication in pTr cells, with the well-recognized immune suppressor SOCS1 validated as a direct target of ssc-miR-149. Overall, this study comprehensively characterized the microRNA-centric regulation of JEV infection in pTr cells, which provides mechanistical insights into JEV infection in pig placenta and will facilitate the development of novel therapies against JEV infection.